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Yorodumi- PDB-7u3b: Structure of S. venezuelae GlgX bound to c-di-GMP and acarbose (p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7u3b | ||||||
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Title | Structure of S. venezuelae GlgX bound to c-di-GMP and acarbose (pH 8.5) | ||||||
Components | Glycogen debranching enzyme GlgX | ||||||
Keywords | HYDROLASE / GlgX / glycogen / acarbose / c-di-GMP / Streptomyces | ||||||
Function / homology | Function and homology information glycogen debranching enzyme activity / glycogen catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / nucleotide binding Similarity search - Function | ||||||
Biological species | Streptomyces venezuelae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.6 Å | ||||||
Authors | Schumacher, M.A. / Tschowri, N. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Allosteric regulation of glycogen breakdown by the second messenger cyclic di-GMP. Authors: Schumacher, M.A. / Wormann, M.E. / Henderson, M. / Salinas, R. / Latoscha, A. / Al-Bassam, M.M. / Singh, K.S. / Barclay, E. / Gunka, K. / Tschowri, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7u3b.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7u3b.ent.gz | 895.5 KB | Display | PDB format |
PDBx/mmJSON format | 7u3b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7u3b_validation.pdf.gz | 5.3 MB | Display | wwPDB validaton report |
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Full document | 7u3b_full_validation.pdf.gz | 5.4 MB | Display | |
Data in XML | 7u3b_validation.xml.gz | 200.8 KB | Display | |
Data in CIF | 7u3b_validation.cif.gz | 264.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u3/7u3b ftp://data.pdbj.org/pub/pdb/validation_reports/u3/7u3b | HTTPS FTP |
-Related structure data
Related structure data | 7u39C 7u3aSC 7u3dC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 80167.234 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces venezuelae (bacteria) / Gene: glgX, DEJ46_08920 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5P2ALW6 #2: Chemical | ChemComp-A16 / #3: Chemical | ChemComp-C2E / #4: Chemical | ChemComp-PO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.67 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 50% MPD, 0.1 M Tris pH 8.5 and 200 mM ammonium phosphate monobasic |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→48.5 Å / Num. obs: 83324 / % possible obs: 98.2 % / Redundancy: 1.7 % / CC1/2: 0.923 / Rpim(I) all: 0.17 / Rsym value: 0.199 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 3.6→3.78 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 5752 / CC1/2: 0.667 / Rpim(I) all: 0.517 / Rsym value: 0.78 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7U3A Resolution: 3.6→48.5 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.67 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 216.7 Å2 / Biso mean: 46.8686 Å2 / Biso min: 0.12 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.6→48.5 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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